Yet another misassembly?

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drevie
Posts: 67
Joined: Sun Feb 04, 2007 10:23 pm
Location: California Lutheran University, Thousand Oaks, CA

Yet another misassembly?

Post by drevie » Tue Mar 20, 2012 6:24 pm

1492J04 also appears to be a misassembly. Although the initial assembly seemed to be okay, with one contig having both ends and not a lot of repeats, the restriction digests suggest that 1.7-2 kb are missing near one end. There is a repeat at the ends of 5/6 that seems to be missing reads in the middle, and contig 4 doesn't seem to fit (the fosmid end is at the left end of 5). Do you have more reads that might fix the problems?
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1492J04-misassembly.JPG
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wleung
Posts: 185
Joined: Sun Feb 04, 2007 7:41 pm
Location: Washington University in St. Louis

Re: Yet another misassembly?

Post by wleung » Wed Mar 21, 2012 8:10 pm

After removing the assembly piece, incorporating all the additional reaction results, and re-running phredPhrap, the restriction digests suggests that there is an extra 2.4kb in the in-silico digests compared to the real digests:
in_silico_larger_real_fragment.png
in silico fragment larger than real
in_silico_larger_real_fragment.png (111.45 KiB) Viewed 5264 times
After analyzing the high quality discrepancies and removing the unaligned high quality reads, I found a join between the two contigs that would resolve the misassembly:
in_silico_after_force_join1492J04.png
in silico digest after force join
in_silico_after_force_join1492J04.png (110 KiB) Viewed 5264 times
Consequently, I do not believe that there are additional reads that are missing from the project.

drevie
Posts: 67
Joined: Sun Feb 04, 2007 10:23 pm
Location: California Lutheran University, Thousand Oaks, CA

Re: Yet another misassembly?

Post by drevie » Thu Mar 22, 2012 12:36 pm

I forgot to suggest removing asmpiece and reassembling. Thanks.

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